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    88 repositories

    • paste3

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•8•1•Updated Nov 25, 2024Nov 25, 2024

    • hatchet

      Public
      HATCHet (Holistic Allele-specific Tumor Copy-number Heterogeneity) is an algorithm that infers allele and clone-specific CNAs and WGDs jointly across multiple tumor samples from the same patient, and that leverages the relationships between clones in these samples.
      Roff
      •
      BSD 3-Clause "New" or "Revised" License
      •32•69•56•5•Updated Nov 25, 2024Nov 25, 2024

    • raphael-group.github.io

      Public
      Raphael group website.
      HTML
      •2•0•0•0•Updated Nov 24, 2024Nov 24, 2024

    • dialect

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Nov 23, 2024Nov 23, 2024

    • LAML

      Public
      LAML is a maximum likelihood algorithm to infer cell phylogeny from dynamic lineage tracing data
      single-cellphylogenymaximum-likelihood-estimationtree-inferencelineage-tracing
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•5•0•0•Updated Nov 22, 2024Nov 22, 2024

    • MERLIN

      Public
      Python
      •0•7•2•0•Updated Nov 19, 2024Nov 19, 2024

    • FRLC

      Public
      Low-rank optimal transport through factor relaxation with latent coupling.
      Jupyter Notebook
      •0•2•0•0•Updated Nov 13, 2024Nov 13, 2024

    • chisel

      Public
      CHISEL -- Copy-number Haplotype Inference in Single-cell by Evolutionary Links
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •11•37•6•1•Updated Nov 13, 2024Nov 13, 2024

    • tree-labeling-polytope

      Public
      Python
      •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

    • SIID

      Public
      Joint imputation and deconvolution across two spatial datasets
      Jupyter Notebook
      •0•1•0•0•Updated Nov 4, 2024Nov 4, 2024

    • GASTON-Mix

      Public
      Python
      •0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

    • HM-OT

      Public
      Hidden Markov Optimal Transport: learning the sequence of latent cell-states and transitions in transcriptomic time-series.
      Jupyter Notebook
      •0•1•0•0•Updated Oct 29, 2024Oct 29, 2024

    • Phyllochron

      Public
      Phyllochron is an ILP method that solves the Maximum Likelihood Longitudinal Assignment Problem under the Longitudinally Observed Perfect Phylogeny Model.
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated Oct 25, 2024Oct 25, 2024

    • chimeric-epistasis

      Public
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 13, 2024Oct 13, 2024

    • fastBE

      Public
      ultrafast phylogenetic reconstruction from bulk DNA sequencing data
      Jupyter Notebook
      •0•5•0•0•Updated Oct 8, 2024Oct 8, 2024

    • lazac-copy-number

      Public
      fast and accurate phylogenetic reconstruction from copy number data
      C++
      •0•6•1•0•Updated Sep 25, 2024Sep 25, 2024

    • DeST_OT

      Public
      Developmental Spatiotemporal Optimal Transport
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•6•0•0•Updated Sep 16, 2024Sep 16, 2024

    • CalicoST

      Public
      Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•21•1•2•Updated Sep 10, 2024Sep 10, 2024

    • MOLLUSC

      Public
      Maximum Likelihood Estimation Of Lineage and Location Using Single Cell Spatial Lineage tracing Data
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 4, 2024Sep 4, 2024

    • startle

      Public
      cellular lineage reconstruction from lineage tracing data
      C++
      •
      MIT License
      •1•4•0•0•Updated Sep 4, 2024Sep 4, 2024

    • copulacci

      Public
      Jupyter Notebook
      •0•4•2•0•Updated Sep 4, 2024Sep 4, 2024

    • GASTON

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•16•0•0•Updated Aug 29, 2024Aug 29, 2024

    • CARTA

      Public
      Jupyter Notebook
      •1•1•0•0•Updated Aug 21, 2024Aug 21, 2024

    • ConDoR

      Public
      Python
      •
      MIT License
      •1•8•0•1•Updated Aug 21, 2024Aug 21, 2024

    • laml-experiments

      Public
      experiments for the LAML paper
      Jupyter Notebook
      •0•0•0•0•Updated Aug 14, 2024Aug 14, 2024

    • STARCH

      Public
      Spatial Transcriptomics Algorithm Reconstructing Copy-number Heterogeneity
      Python
      •
      MIT License
      •9•20•10•1•Updated Jul 22, 2024Jul 22, 2024

    • decifer

      Public
      DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•20•8•0•Updated May 21, 2024May 21, 2024

    • hetdetect

      Public
      Inferring Het SNP positions from tumor samples using Hidden Markov Models
      Python
      •1•0•0•0•Updated May 3, 2024May 3, 2024

    • sc-mail-experiments

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Apr 8, 2024Apr 8, 2024

    • hatchet2-simulations

      Public
      Snakemake pipeline for generating and running on new simulated data for HATCHet2 revisions
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Apr 2, 2024Apr 2, 2024